Interpretive Summary: Molecular genetic maps provide the basis for identifying economically important genes such as those involved in growth, reproduction, and disease resistance. The utility of a genetic map is dependent on the number of genetic markers. To increase the accuracy and applicability of the East Landing chicken genetic map, a new type of marker called amplified fragment length polymorphic or AFLP was investigated. As a result, the number of mapped genetic markers increased by over 200 with potentially many more easily placed. This study shows that AFLP markers are highly informative and useful in genetic mapping. The scoring of these markers in other chicken populations also indicates that about 40% of these markers are readily portable. The increased saturation of the East Lansing map enables scientists in industry and academia to more easily screen the chicken genome for agriculturally important genes, which will ultimately benefit the consumer by providing ecomomical and safe poultry products.

Technical Abstract:
The AFLP (Amplified Fragment Lenght Polymorphism) technique has been used to enhance marker density in the East Lansing reference chicken genome map, based on a backcross family derived from a Red Jungle Fowl by White Leghorn mating with White Leghorn as the recurrnet parent. To date, 204 AFLP markers have been added, over 20% of all markers presently on this map. AFLP are about 60% as frequent in a cross with White Leghorns (Line 72 X 63) in comparison to the more divergent reference map population. Based on apparent identity of size, about 40% of the line 72 X 63 cross AFLP fragent also were observed in the reference map cross. Primer paris in which one primer contains 3' extensions of three selective nucleotides and the other has two selective nucleotides successfully generate AFLP from chicken DNA, but such pairs appear to amplify only a subset of those fragments to which they have an exact sequence match. Three different restriction enzymes with four base pair recognition sites (TAQI, HINPI and MSPI) were found to work well with ECORI as the rarer of the two AFLP restriction enzymes used, with HINPI being the most effective of the three. AFLP markers are likely to provide an economical method with which to enhance framework linkage maps of chicken and probably other avian genomes.